I'm not the super fan that has listened to all of the writer talks or digested all of Gateworld et al, but I would like to know how much writers had developed McKay in SG-1, and how they plotted his growth with Atlantis becoming a series.

The growth of that character is one of my favorite things about the franchise. David played him so well--no character made me cry as much as McKay, because I think I (and likely many others) relate to him! I'm autistic, and I also get myopic and hyper-fixated and think I know everything and yes, it's arrogance, but I often have little control over it. However,like him, I've learned to manage my tics and, over time, alter my behavior to be more sociable.

Regarding OP's main question: I thought it was absolutely heinous how he acted! He was playing the typical STEM misogynist, and he played it to a T. I'm a millennial, and where I was at in my life, I completely missed SG-1 on it's original airing, so my introduction to the Stargate TV series(es) was actually in passing in the break room at my work, and it was Atlantis, on Comet, riddled with commercial breaks, so I loathed his character at first.
Then, the pandemic happened, and I had Netflix (which SG-1 was on). I binged the series, and HATED McKay even, because he was even worse in SG-1! But then, I finished SG-1 & I moved onto Atlantis.

I was ready to keep hating him--but I was actually able to watch Atlantis in without distraction or having to rush back to work. McKay was finally given tremendous responsibilities. People depended on him DAILY. The Shrine??? HELLO??? David Hewlett and his sister Kate had me WEEPING. Such a fucking heartfelt episode, and I'm honestly crying right now, thinking about it.

I completely agree with you, OP. McKay may be my favorite character in the franchise, and it's because of the writers and the actor just knocking it outta the fucking park. I love the Rodney McKay (and, para-socially, David Hewlett, who is such a cool guy IMO).